Using the source they provide, yes, if you limit to WP 2.5 you get 3. If you leave it as any version you get what they reported, 42. For MT the only choice is any and you get zero for 2008.
It's an apples to apples comparison by a neutral third party, namely the US government. 42 vulnerabilities in all versions of WP so far this year, zero in all versions of MT. Total WP has 122 since 2004, MT has had 11 since 2003 for all versions of either platform.
That said, the statistics are perhaps a bit misleading taken at face value, and there is a good discussion of why that may be true in the comments of that post. In short, the numbers include not just WP but plugins as well (same for MT, but there are a lot more WP plugins I guess), and because WP has been open source from the start and MT is only recently, there may have been better reporting for WP vs. MT. Matt (I assume from Automatic/WP) points out that there have been 3 security issues in MT this year, but the stats quoted don't show any. Anil counters with his own arguments on why looking at the big picture, plugins and all, is valid.
So I agree, you need to be careful with the stats and understand what you are looking at. I think even taking those things into account, MT has a better track record of security.